The genetic architecture underlying natural variation in complex trait assemblages is not well understood. Elucidating this architecture could contribute greatly to our knowledge of the mechanisms promoting developmental and behavioral diversity and novelty, as well as provide models for understanding genetically based variation in complex human traits. The proposed project aims to develop linkage and QTL maps in the Drosophila elegans/gunungcola species pair to determine the molecular genetic basis of intra- and interspecies variation in body color and interspecies divergence in two male-specific traits, wing spots and wing courtship display, that are tightly evolutionarily associated. Specifically, this work is designed to address three longstanding questions on the origins and dynamics of morphogenetic and behavioral diversity. First, deciphering the genetics of pigmentation and behavioral divergence in these species will provide important insights on the types of loci and alleles underlying the responses of morphogenetic and behavioral pathways to natural and sexual selection. Second, mapping the positions of quantitative trait loci (QTLs) for each trait will help to reveal whether the genetic architectures of evolutionarily associated traits are independent or connected by linkage or pleiotropy. Third, comparing the genetic basis of body color variation within and between species will indicate whether the mechanisms underlying between-species divergence are similar to or distinct from those underlying within-species polymorphism, thus testing a main tenet of the neo-Darwinian evolutionary synthesis. These questions are also of great interest to developmental and behavioral biologists, who seek to determine the molecular genetic basis of complex, species-specific phenotypes and whether genetic information from model species can be applied across taxa. Because evolutionary change in male wing pigment patterns and display behaviors has occurred repeatedly in the Oriental melanogaster group lineages, our results will also enable us to investigate whether independent cases of pigmentation and courtship evolution involve similar or distinct genetic underpinnings.